RNA Velocity using scVelo¶

Marissa Esteban

Data: CITEseq YS006_UW

I did pre processing in Suerat and saved object as .h5Seurat to perform RNAvelo in Python wtih scVelo

In [1]:
# Setup
import scanpy as sc
import scvelo as scv
import anndata
import loompy
import mygene
import scipy
import seaborn as sns
import matplotlib.pyplot as plt
In [3]:
h5ad_path = "/Volumes/PortableSSD/IntegratedMultimodal_CITEseq.h5ad"
adata = sc.read_h5ad(h5ad_path)
adata.obs.index = [x.split('-')[0] for x in adata.obs.index]    # TTTGGAGTCGGTTGTA-1_1

loom_paths = ["/Volumes/PortableSSD/YS001/possorted_genome_bam_KLWV0.loom",
              "/Volumes/PortableSSD/YS002/possorted_genome_bam_PNEM4.loom",
              "/Volumes/PortableSSD/YS003/possorted_genome_bam_8Q2XV.loom",
              "/Volumes/PortableSSD/YS004/possorted_genome_bam_0XB2N.loom",
              "/Volumes/PortableSSD/YS005/possorted_genome_bam_HX08G.loom",
              "/Volumes/PortableSSD/YS006/possorted_genome_bam_751VB.loom"]
combined_loom_path = "/Volumes/PortableSSD/citeseq_combined.loom"

loompy.combine(loom_paths, combined_loom_path)
ldata = sc.read_loom(combined_loom_path)
ldata.obs.index = [x.split(':')[1] for x in ldata.obs.index]    # possorted_genome_bam_751VB:AAAGTCCGTAAGGTCGx
ldata.obs.index = [x[:-1] for x in ldata.obs.index] 

WARNING:root:╭── 'batch_scan_layers' is deprecated. Use 'scan' instead
WARNING:root:╰──> at /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/loompy/loompy.py, line 471
WARNING:root:╭── 'batch_scan_layers' is deprecated. Use 'scan' instead
WARNING:root:╰──> at /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/loompy/loompy.py, line 471
WARNING:root:╭── 'batch_scan_layers' is deprecated. Use 'scan' instead
WARNING:root:╰──> at /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/loompy/loompy.py, line 471
WARNING:root:╭── 'batch_scan_layers' is deprecated. Use 'scan' instead
WARNING:root:╰──> at /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/loompy/loompy.py, line 471
WARNING:root:╭── 'batch_scan_layers' is deprecated. Use 'scan' instead
WARNING:root:╰──> at /opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/loompy/loompy.py, line 471

SANITY CHECKING¶

  • inspecting andata and ldata objects (cell and gene counts)
  • checking for duplicates
In [4]:
print("=== Seurat-derived AnnData (adata) ===")
print("Cells (obs):", adata.n_obs)
print("Genes (var):", adata.n_vars)
print("\nFirst 10 cell names:", adata.obs.index[:10].tolist())
print("\nFirst 10 gene names:", adata.var.index[:10].tolist())

print("\n\n=== Loom RNA velocity AnnData (ldata) ===")
print("Cells (obs):", ldata.n_obs)
print("Genes (var):", ldata.n_vars)
print("\nFirst 10 cell names:", ldata.obs.index[:10].tolist())
print("\nFirst 10 gene names:", ldata.var.index[:10].tolist())

print("\n\n=== Layer shapes in ldata ===")
for layer in ["spliced", "unspliced", "ambiguous"]:
    if layer in ldata.layers:
        print(f"{layer}: {ldata.layers[layer].shape}")



# check for duplicates in adata and ladata
print("\n\n=== Checking for dupicates ===")
print("Total cells in adata:", len(adata.obs.index))
print("Unique cells in adata:", len(adata.obs.index.unique()))
print("Duplicate barcodes in adata:", len(adata.obs.index) - len(adata.obs.index.unique()))

print("\nTotal cells in ldata:", len(ldata.obs.index))
print("Unique cells in ldata:", len(ldata.obs.index.unique()))
print("Duplicate barcodes in ldata:", len(ldata.obs.index) - len(ldata.obs.index.unique()))

# Show some duplicates if they exist
from collections import Counter
adata_counts = Counter(adata.obs.index)
adata_duplicates = {bc: count for bc, count in adata_counts.items() if count > 1}
print(f"\nNumber of duplicated barcodes: {len(adata_duplicates)}")
if adata_duplicates:
    print("Examples:", list(adata_duplicates.items())[:5])

=== Seurat-derived AnnData (adata) ===
Cells (obs): 35317
Genes (var): 30481

First 10 cell names: ['AAACCCAAGAACAGGA', 'AAACCCAAGTCTCTGA', 'AAACGAAAGACTACGG', 'AAACGAAAGATTCGCT', 'AAACGAAAGCTCACTA', 'AAACGAACAGCTGTAT', 'AAACGAACATCCTTGC', 'AAACGAAGTACTGACT', 'AAACGAAGTGTATCCA', 'AAACGAAGTTGCTCGG']

First 10 gene names: ['Xkr4', 'Gm19938', 'Sox17', 'Mrpl15', 'Lypla1', 'Tcea1', 'Rgs20', 'Atp6v1h', 'Npbwr1', '4732440D04Rik']


=== Loom RNA velocity AnnData (ldata) ===
Cells (obs): 45487
Genes (var): 33696

First 10 cell names: ['AAAGGGCAGTCATACC', 'AAAGGTATCGGAAGGT', 'AAATGGACACTCAAGT', 'AAAGAACCAGTTGTTG', 'AAACGAACATCCTTGC', 'AAAGGATTCCAATCTT', 'AAATGGAAGTGGAAAG', 'AAAGTCCAGAACGCGT', 'AAAGTGAGTCACGTGC', 'AAAGGGCGTTGTCTAG']

First 10 gene names: ['ENSMUSG00000079800', 'ENSMUSG00000095092', 'ENSMUSG00000079794', 'ENSMUSG00000079192', 'ENSMUSG00000094799', 'ENSMUSG00000095250', 'ENSMUSG00000095787', 'ENSMUSG00000095672', 'ENSMUSG00000094514', 'ENSMUSG00000096100']


=== Layer shapes in ldata ===
spliced: (45487, 33696)
unspliced: (45487, 33696)
ambiguous: (45487, 33696)


=== Checking for dupicates ===
Total cells in adata: 35317
Unique cells in adata: 35173
Duplicate barcodes in adata: 144

Total cells in ldata: 45487
Unique cells in ldata: 45252
Duplicate barcodes in ldata: 235

Number of duplicated barcodes: 143
Examples: [('AAACGAAAGATTCGCT', 2), ('AAACGAATCTCAACCC', 2), ('AACAAGAGTACCTAGT', 2), ('AAGCATCTCGTCAGAT', 2), ('AATGGCTTCGCTAATG', 2)]
In [5]:
# Remove duplicates from both datasets (keep first occurrence)
print("\n=== Removing duplicates ===")
adata = adata[~adata.obs.index.duplicated(keep='first'), :]
ldata = ldata[~ldata.obs.index.duplicated(keep='first'), :]

print(f"adata after dedup: {adata.shape}")
print(f"ldata after dedup: {ldata.shape}")

# Find common barcodes
common_barcodes = set(adata.obs.index).intersection(set(ldata.obs.index))
print(f"\n=== Common cells ===")
print(f"Cells in common: {len(common_barcodes)}")

# Subset both datasets to only common cells
# Convert to list and sort for reproducibility
common_barcodes = sorted(list(common_barcodes))

adata = adata[common_barcodes, :]
ldata = ldata[common_barcodes, :]

print(f"\n=== Final datasets ===")
print(f"Final adata shape: {adata.shape}")
print(f"Final ldata shape: {ldata.shape}")
print(f"Indices match: {all(adata.obs.index == ldata.obs.index)}")

=== Removing duplicates ===
adata after dedup: (35173, 30481)
ldata after dedup: (45252, 33696)

=== Common cells ===
Cells in common: 34946

=== Final datasets ===
Final adata shape: (34946, 30481)
Final ldata shape: (34946, 33696)
Indices match: True
In [6]:
# converting the loom's ENSEMBL ID's to match 

mg = mygene.MyGeneInfo()
gene_index = ldata.var.index.to_series()

# only grab the genes that have ENSEMBL IDs
is_ensembl = gene_index.str.startswith("ENSMUSG")

print("Total genes:", gene_index.shape[0])
print("ENSEMBL-like genes:", is_ensembl.sum())
print("Already-symbol-like genes:", (~is_ensembl).sum(), '\n')

# only query the ENSMUSG IDs
ens_ids = gene_index[is_ensembl].unique().tolist()

results = mg.querymany(
    ens_ids,
    scopes="ensemblgene",   # or "ensembl.gene" depending on mygene version, but this usually works
    fields="symbol",
    species="mouse",
    as_dataframe=False
)

# Build mapping dict ENSMUSG -> symbol
ens_to_symbol = {r["query"]: r.get("symbol", None) for r in results}

# QC on mapping
total_ens = len(ens_ids)
mapped_ens = sum(v is not None for v in ens_to_symbol.values())
print("Total ENSMUSG IDs:", total_ens)
print("Mapped ENSMUSG → symbol:", mapped_ens)
print("Unmapped ENSMUSG:", total_ens - mapped_ens)

# 4) Create a 'symbol' column:
# default: keep existing name
ldata.var["symbol"] = gene_index.copy()

# replace ENSMUSG entries with their symbol
for g in gene_index[is_ensembl]:
    sym = ens_to_symbol.get(g, None)
    if sym is not None:
        ldata.var.at[g, "symbol"] = sym


ldata.var.index = ldata.var["symbol"]

gene_index = ldata.var.index.to_series()
is_ensembl = gene_index.str.startswith("ENSMUSG")

print("Total ENSMUSG IDs after mapping: ", is_ensembl.sum())

WARNING:biothings.client:Input sequence provided is already in string format. No operation performed
WARNING:biothings.client:Input sequence provided is already in string format. No operation performed
INFO:biothings.client:querying 1-248 ...

Total genes: 33696
ENSEMBL-like genes: 248
Already-symbol-like genes: 33448 


INFO:biothings.client:Finished.
WARNING:biothings.client:13 input query terms found no hit:	['ENSMUSG00000095742', 'ENSMUSG00000095728', 'ENSMUSG00000095076', 'ENSMUSG00000121317', 'ENSMUSG000
INFO:biothings.client:Pass "returnall=True" to return complete lists of duplicate or missing query terms.

Total ENSMUSG IDs: 248
Mapped ENSMUSG → symbol: 203
Unmapped ENSMUSG: 45
Total ENSMUSG IDs after mapping:  45
In [7]:
# Intersect with Seurat genes
ldata.var_names_make_unique()  # This handles any duplicate gene symbol

print("Total number of var names: ", len(adata.var_names))

# Now find common genes between the two datasets
common_genes = adata.var.index.intersection(ldata.var.index)
print("Overlapping genes after symbol mapping:", len(common_genes))

# Subset both datasets to common genes
adata_subset = adata[:, common_genes].copy()
ldata_subset = ldata[:, common_genes].copy()

print(f"adata shape: {adata_subset.shape}")
print(f"ldata shape: {ldata_subset.shape}")

Total number of var names:  30481
Overlapping genes after symbol mapping: 29365
adata shape: (34946, 29365)
ldata shape: (34946, 29365)
In [8]:
# Sanity Checks

# Verify cell barcodes match
print("Cells match:", (adata_subset.obs.index == ldata_subset.obs.index).all())

# If they don't match, reorder ldata_subset to match adata_subset:
ldata_subset = ldata_subset[adata_subset.obs.index, :].copy()

# Double-check genes are in same order
print("Genes match:", (adata_subset.var.index == ldata_subset.var.index).all())

Cells match: True
Genes match: True

Integrating Loom and OWHA object¶

In [9]:
# Add velocity layers to adata_subset
adata_subset.layers["spliced"] = ldata_subset.layers["spliced"].copy()
adata_subset.layers["unspliced"] = ldata_subset.layers["unspliced"].copy()
adata_subset.layers["ambiguous"] = ldata_subset.layers["ambiguous"].copy()

# Verify they were added
print("Layers in adata_subset:", list(adata_subset.layers.keys()))
print("Spliced shape:", adata_subset.layers["spliced"].shape)
print("Unspliced shape:", adata_subset.layers["unspliced"].shape)

Layers in adata_subset: ['spliced', 'unspliced', 'ambiguous']
Spliced shape: (34946, 29365)
Unspliced shape: (34946, 29365)
In [10]:
adata_subset.obs
Out[10]:
orig.ident nCount_RNA nFeature_RNA timepoint nCount_ADT nFeature_ADT percent_mito percent_ribo timepoint_modality nCount_SCT ... gptcelltype sctype_skinDB singleR celltype celltype_fine metaclusters StressScore1 TF percentage nCount_RNA_v4 nFeature_RNA_v4
AAACCCAAGAACAGGA UW_CITEseq_1 4246.0 1723 Unwounded 399.0 78 8.431465 6.947715 Unwounded_CITEseq 8358.0 ... Fibroblasts Cycling cells Cardiomyocytes Pericytes Pericyte II Pericytes 0.975801 7.348092 4246.0 1723
AAACCCAAGATACAGT D30PW_CITEseq_1 5424.0 2026 Wounded_D30PW 239.0 69 5.530973 6.526549 Wounded_D30PW_CITEseq 7201.0 ... Keratinocytes Cycling cells Neurons HF Keratinocytes IRS II HF Keratinocytes 0.010937 8.001475 5424.0 2026
AAACCCAAGCAATAGT D15PW_CITEseq_2 5251.0 1547 Wounded_D15PW 1507.0 98 1.256903 26.128357 Wounded_D15PW_CITEseq 6036.0 ... Keratinocytes Unknown T cells Dendritic cells cDC2 Immune cells -0.038145 3.446962 5251.0 1547
AAACCCAAGCGCCTAC D15PW_CITEseq_2 6564.0 2217 Wounded_D15PW 1846.0 99 1.416819 12.568556 Wounded_D15PW_CITEseq 6529.0 ... Keratinocytes Schwann cells Microglia Macrophages Neutrophils II Immune cells 0.267384 6.230957 6564.0 2217
AAACCCAAGCTAGTTC D15PW_CITEseq_1 6762.0 2138 Wounded_D15PW 1862.0 100 1.286602 12.407572 Wounded_D15PW_CITEseq 6697.0 ... Fibroblasts Unknown Microglia Macrophages Macrophages III Immune cells 0.501483 4.702751 6762.0 2138
... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
TTTGTTGTCTCAGTCC D30PW_CITEseq_1 16213.0 3284 Wounded_D30PW 260.0 66 1.443286 32.757664 Wounded_D30PW_CITEseq 8354.0 ... Keratinocytes Suprabasal Keratinocytes B cells IFE Keratinocytes Spinous I IFE Keratinocytes 0.377910 3.904274 16213.0 3284
TTTGTTGTCTCTGCTG D30PW_CITEseq_2 15672.0 4255 Wounded_D30PW 628.0 85 3.088310 24.183257 Wounded_D30PW_CITEseq 5257.0 ... Schwann cells Cycling cells Erythrocytes Proliferating Keratinocytes Ker.Cycling II HF Keratinocytes 0.220671 6.202144 15672.0 4255
TTTGTTGTCTGCGAGC D15PW_CITEseq_2 14728.0 3067 Wounded_D15PW 1545.0 101 2.783813 27.206681 Wounded_D15PW_CITEseq 6825.0 ... Unknown Suprabasal Keratinocytes Oligodendrocytes IFE Keratinocytes Spinous III IFE Keratinocytes 0.167667 3.102933 14728.0 3067
TTTGTTGTCTGGAAGG D15PW_CITEseq_1 5141.0 1741 Wounded_D15PW 1740.0 97 1.225443 0.641898 Wounded_D15PW_CITEseq 5966.0 ... Keratinocytes Fibroblasts Astrocytes Fibroblasts Nfkb+ Fibroblasts Fibroblasts 0.005348 9.258899 5141.0 1741
TTTGTTGTCTGGTGGC D15PW_CITEseq_1 3119.0 1472 Wounded_D15PW 1602.0 98 1.090093 9.009298 Wounded_D15PW_CITEseq 6053.0 ... Keratinocytes Macrophages Microglia Macrophages Macrophages III Immune cells 0.523043 6.572619 3119.0 1472

34946 rows × 28 columns

In [11]:
adata_subset.layers.keys()
Out[11]:
KeysView(Layers with keys: spliced, unspliced, ambiguous)

Starting RNA Velocity!¶

Now that we have combined the .loom file with our exported Seurat object (now AnnData object) we can explore with RNA Velocity

In [12]:
adata_subset.obsm.keys()
Out[12]:
KeysView(AxisArrays with keys: X_cca, X_harmony, X_pca, X_rpca, X_umap.cca, X_umap.harmony, X_umap.pca, X_umap.rpca)
In [13]:
# plot umap to check
adata_subset.obsm["X_umap"] = adata_subset.obsm["X_umap.rpca"].copy()

sc.pl.umap(adata_subset, color="celltype", frameon=False,
           legend_loc='on data', title='', save='_celltypes_rpca.pdf')

WARNING: saving figure to file figures/umap_celltypes_rpca.pdf
No description has been provided for this image
In [14]:
scv.pl.proportions(adata_subset, groupby='celltype')
No description has been provided for this image
In [15]:
adata_subset.obsm["X_pca"].shape
Out[15]:
(34946, 50)
In [16]:
# pre-process
scv.pp.filter_and_normalize(adata_subset, min_shared_counts=20)
sc.pp.highly_variable_genes(adata_subset, n_top_genes=2000)

# subset to HVGs
adata_hvg = adata_subset[:, adata_subset.var['highly_variable']].copy()

# recompute neighbors on HVG PCA
scv.pp.moments(adata_hvg, n_pcs=30, n_neighbors=30)

Filtered out 17472 genes that are detected 20 counts (shared).
WARNING: Did not normalize X as it looks processed already. To enforce normalization, set `enforce=True`.
Normalized count data: spliced, unspliced.

/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/preprocessing/utils.py:705: DeprecationWarning: `log1p` is deprecated since scVelo v0.3.0 and will be removed in a future version. Please use `log1p` from `scanpy.pp` instead.
  log1p(adata)

Logarithmized X.

/var/folders/hq/r4mfshzj3dq22fq4382_72qw0000gp/T/ipykernel_20518/1409331441.py:9: DeprecationWarning: Automatic neighbor calculation is deprecated since scvelo==0.4.0 and will be removed in a future version of scVelo. Please compute neighbors first with Scanpy.
  scv.pp.moments(adata_hvg, n_pcs=30, n_neighbors=30)
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/preprocessing/moments.py:71: DeprecationWarning: `neighbors` is deprecated since scvelo==0.4.0 and will be removed in a future version of scVelo. Please compute neighbors with Scanpy.
  neighbors(

computing neighbors
    finished (0:00:13) --> added 
    'distances' and 'connectivities', weighted adjacency matrices (adata.obsp)
computing moments based on connectivities
    finished (0:00:02) --> added 
    'Ms' and 'Mu', moments of un/spliced abundances (adata.layers)
In [17]:
# compute velocity ( this step will take a while )
try:
    scv.tl.recover_dynamics(adata_hvg, n_top_genes=500)
    scv.tl.velocity(adata_hvg, mode='dynamical')
    scv.tl.velocity_graph(adata_hvg)
except Exception as e:
    print("Error while fitting dynamics:", e)
    print("Current gene index:", adata_hvg.var_names[adata_hvg.var['fit_alpha'].isna()].tolist()[:10])

recovering dynamics (using 1/16 cores)
WARNING: Unable to create progress bar. Consider installing `tqdm` as `pip install tqdm` and `ipywidgets` as `pip install ipywidgets`,
or disable the progress bar using `show_progress_bar=False`.
    finished (0:11:37) --> added 
    'fit_pars', fitted parameters for splicing dynamics (adata.var)
computing velocities
    finished (0:00:04) --> added 
    'velocity', velocity vectors for each individual cell (adata.layers)
computing velocity graph (using 1/16 cores)
    finished (0:00:11) --> added 
    'velocity_graph', sparse matrix with cosine correlations (adata.uns)
In [18]:
scv.pl.velocity_embedding_grid(
    adata_hvg,
    basis='X_umap',     
    color='celltype',
    dpi=150
)

computing velocity embedding
    finished (0:00:01) --> added
    'velocity_umap', embedded velocity vectors (adata.obsm)

/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
No description has been provided for this image
In [19]:
scv.pl.velocity_embedding(adata_hvg, 
                          arrow_length=3, 
                          arrow_size=2, 
                          color='celltype',
                          dpi=120)

/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
No description has been provided for this image
In [20]:
scv.tl.rank_velocity_genes(adata_hvg, groupby='celltype')
df = scv.get_df(adata_hvg.uns['rank_velocity_genes']['names'])
df.head()

ranking velocity genes

/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/tools/utils.py:463: DeprecationWarning: Please import `rankdata` from the `scipy.stats` namespace; the `scipy.stats.stats` namespace is deprecated and will be removed in SciPy 2.0.0.
  from scipy.stats.stats import rankdata

    finished (0:00:06) --> added 
    'rank_velocity_genes', sorted scores by group ids (adata.uns) 
    'spearmans_score', spearmans correlation scores (adata.var)

/var/folders/hq/r4mfshzj3dq22fq4382_72qw0000gp/T/ipykernel_20518/2477482753.py:2: DeprecationWarning: `get_df` is deprecated since scvelo==0.4.0 and will be removed in a future version of scVelo. Please `AnnData::get_df` or Scanpy's `scanpy.get.obs_df` or `scanpy.get.var_df`.
  df = scv.get_df(adata_hvg.uns['rank_velocity_genes']['names'])
Out[20]:
Neutrophils Dendritic cells Fibroblasts Macrophages IFE Keratinocytes T cells Endothelial cells Proliferating Keratinocytes HF Keratinocytes Muscle cells Pericytes Sebocytes Melanocytes Langerhans cells Proliferating Fibroblasts Schwann cells Mast cells RBCs Proliferating immune cells
0 Laptm5 Basp1 Ugdh Basp1 Anxa1 Lcp2 Mef2c Itga6 Hspg2 Actb Lamc1 Itga6 Zbtb20 Pkib Fstl1 Nid1 Lgals1 Csf2ra Basp1
1 Crem Plek Dst Itgb2 Serpinb2 Tm6sf1 Nid1 Lamc1 Anxa8 Mt1 Zbtb20 Anxa8 Rgl1 Ctsc Fgfr1 Col5a2 Pdpn Actb Crem
2 Tm6sf1 Crem Fgfr1 Emilin2 Plet1 Sp100 Rgl1 Slc7a8 Lamc1 Vim Serpine1 Timp3 Pcolce2 Crem Zbtb20 Zbtb20 Hexa Mt1 Itgb2
3 Epsti1 Itgb2 Fstl1 Slc15a3 Fosb Samhd1 Ebf1 Creb5 Creb5 Col6a2 Col5a2 Serpinb5 Nid1 Tnfaip2 Col5a2 Col6a2 Man1a Tnfaip2 Cd300a
4 Soat1 Lilrb4b Dab2 Lgals3 Epha4 Ms4a4c Cd34 Hspg2 Itga6 Pcolce2 Fstl1 Gata3 Rassf3 Hexa Axl Lama2 Ctsc Ly86 Plek
In [21]:
for cluster in ['IFE Keratinocytes', 'Fibroblasts', 'Proliferating immune cells', 'Proliferating Fibroblasts']:
    scv.pl.scatter(adata_hvg, df[cluster][:5], ylabel=cluster, frameon=False, color='celltype')

/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
No description has been provided for this image 
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
No description has been provided for this image 
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
No description has been provided for this image 
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
No description has been provided for this image
In [23]:
scv.pl.scatter(adata_hvg, color='celltype', basis=adata_hvg.uns["rank_velocity_genes"]["names"]["IFE Keratinocytes"][:3])

/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
No description has been provided for this image
In [24]:
scv.pl.velocity(adata_hvg, ['Epb41l2'], color='celltype')

/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
No description has been provided for this image
In [25]:
scv.pl.velocity(adata_hvg, ['Mki67'], color='celltype') # Proliferating Keratinocytes

/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
No description has been provided for this image
In [26]:
scv.tl.latent_time(adata_hvg)
scv.pl.scatter(adata_hvg, color='latent_time', color_map='gnuplot', size=80)

computing terminal states
    identified 9 regions of root cells and 2 regions of end points .
    finished (0:00:10) --> added
    'root_cells', root cells of Markov diffusion process (adata.obs)
    'end_points', end points of Markov diffusion process (adata.obs)
computing latent time using root_cells as prior
    finished (0:00:03) --> added 
    'latent_time', shared time (adata.obs)

/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
No description has been provided for this image
In [27]:
top_genes = adata_hvg.var['fit_likelihood'].sort_values(ascending=False).index[:300]
scv.pl.heatmap(adata_hvg, var_names=top_genes, sortby='latent_time', col_color='metaclusters', n_convolve=100)

/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
No description has been provided for this image
In [33]:
scv.pl.scatter(adata_hvg, color='latent_time', color_map='viridis')

/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
No description has been provided for this image
In [28]:
top_genes
Out[28]:
Index(['Dmkn', 'Cytip', 'Perp', 'Hmox1', 'Zeb2', 'Fstl1', 'F13a1', 'Serpinb5',
       'Ifi205', 'Oasl1',
       ...
       'Nlrp3', 'Slc7a8', 'Slfn2', 'Actb', 'Igf1', 'Emilin2', 'Tnfaip6',
       'Kitl', 'Col6a2', 'Fcgrt'],
      dtype='object', length=300)
In [29]:
scv.pl.velocity(adata_hvg, ['Cfp'], color='celltype')

/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
No description has been provided for this image
In [30]:
top_genes = adata_hvg.var['fit_likelihood'].sort_values(ascending=False).index
scv.pl.scatter(adata_hvg, basis=top_genes[:15], ncols=5, frameon=False, color='celltype',)

/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
No description has been provided for this image
In [31]:
var_names = ['Zbtb20', 'Celf2']
scv.pl.scatter(adata_hvg, var_names, frameon=False, color='celltype',)
scv.pl.scatter(adata_hvg, x='latent_time', y=var_names, frameon=False, color='celltype',)

/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
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/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
/opt/miniconda3/envs/scvelo_env/lib/python3.10/site-packages/scvelo/plotting/utils.py:68: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead
  return isinstance(c, str) and c in data.obs.keys() and cat(data.obs[c])
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